X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=2e6f5354e1856a47094ab14181e6ae103291eb0b;hb=4967051aa734ece6ce44f0fb891a936e849c2fe2;hp=64df707683cb8c2ee3fb4a6cf7f0612482a37413;hpb=aee93c83c1c7ff30c2c959a14877cf8a4e2d8f92;p=samtools.git diff --git a/ChangeLog b/ChangeLog index 64df707..2e6f535 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,205 @@ +------------------------------------------------------------------------ +r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam.h + M /trunk/samtools/bam_pileup.c + M /trunk/samtools/bam_plcmd.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.7-14 (r591) + * elementary multi-way pileup. More testing and more functionality to be done. + +------------------------------------------------------------------------ +r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam.h + M /trunk/samtools/bam_pileup.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.7-13 (r590) + * added mpileup APIs. No compiling errors, but not tested at all. It is late. + +------------------------------------------------------------------------ +r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam.h + M /trunk/samtools/bam_pileup.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.7-12 (r589) + * added iterator-like APIs for pileup + +------------------------------------------------------------------------ +r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam_index.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.7-11 (r588) + * ported a few improvements from tabix back to samtools + +------------------------------------------------------------------------ +r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam.h + M /trunk/samtools/bam_index.c + M /trunk/samtools/bamtk.c + + * samtools-0.1.7-10 (r587) + * added iterator interface for bam_fetch (ported back from tabix) + +------------------------------------------------------------------------ +r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/Makefile + A /trunk/samtools/bam_reheader.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/bgzf.c + + * samtools-0.1.7-9 (r586) + * added "reheader" to replace the BAM header + +------------------------------------------------------------------------ +r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines +Changed paths: + M /trunk/samtools/bam.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/kstring.h + + * samtools-0.1.7-8 (r585) + * speed up "view" + +------------------------------------------------------------------------ +r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines +Changed paths: + M /trunk/samtools/bam.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/bgzf.c + M /trunk/samtools/bgzf.h + M /trunk/samtools/kstring.h + M /trunk/samtools/misc/wgsim_eval.pl + + * samtools-0.1.7-7 (r584) + * ported tabix BGZF to samtools + * flush BGZF after writing the BAM header and between alignment boundaries + +------------------------------------------------------------------------ +r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line +Changed paths: + A /trunk/samtools/misc/varfilter.py + +Initial release on behalf of Aylwyn Scally +------------------------------------------------------------------------ +r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line +Changed paths: + M /trunk/samtools/samtools.1 + +Added a note about the indels coordinates +------------------------------------------------------------------------ +r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Added the possibility to print or not to print the reference allele +------------------------------------------------------------------------ +r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line +Changed paths: + M /trunk/samtools/sam_header.c + +More descriptive message for space separated tags +------------------------------------------------------------------------ +r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Speedup with -i, no need to query the reference all the time +------------------------------------------------------------------------ +r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line +Changed paths: + M /trunk/samtools/sam_header.c + +Fixed the order of sequences in the header +------------------------------------------------------------------------ +r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Added possibility to select indels only and fixed a bug in reporting homozygous indels. +------------------------------------------------------------------------ +r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines +Changed paths: + M /trunk/samtools/bam.c + +Improve the invalid 'BAM\1' magic number error message, and also print it +when no bytes can be read from the alleged BAM file, e.g., in the common +user error case when a SAM file has accidentally been supplied. + +------------------------------------------------------------------------ +r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/AUTHORS + M /trunk/samtools/bam.h + M /trunk/samtools/bam_import.c + M /trunk/samtools/sam_header.c + +Improved efficiency of header parsing +------------------------------------------------------------------------ +r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines +Changed paths: + M /trunk/samtools/misc/export2sam.pl + +Updated export2sam.pl by Chris Saunders from Illumina. + + +------------------------------------------------------------------------ +r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/samtools.pl + +Fixed filtering of SNPs near indels. Added min indel and SNP quality filter. +------------------------------------------------------------------------ +r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Print an error for pileups in simple format +------------------------------------------------------------------------ +r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines +Changed paths: + M /trunk/samtools/bam_plcmd.c + +added a hidden option in pileup to output the base position (for Erin) + +------------------------------------------------------------------------ +r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Added possibility to specify a custom column title for the data column +------------------------------------------------------------------------ +r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/bam_plcmd.c + +Added the -d option to limit maximum depth for indels. +------------------------------------------------------------------------ +r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line +Changed paths: + M /trunk/samtools/misc/sam2vcf.pl + +Added VCF header +------------------------------------------------------------------------ +r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines +Changed paths: + M /trunk/samtools/ChangeLog + M /trunk/samtools/bam_plcmd.c + M /trunk/samtools/bamtk.c + M /trunk/samtools/misc/samtools.pl + M /trunk/samtools/misc/wgsim.c + + * samtools-0.1.7-6 + * fixed a bug in faidx + ------------------------------------------------------------------------ r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines Changed paths: